Detection of evolutionary conserved and accelerated genomic regions related to adaptation to thermal niches in Anolis lizards.

Full text Figures and data Side by side Abstract Editor's evaluation Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Functionally indispensable genes are likely to be retained and otherwise to be lost during evolution. This evolutionary fate of a gene can also be affected by factors independent of gene dispensability, including the mutability of genomic positions, but such features have not been examined well. To uncover the genomic features associated with gene loss, we investigated the characteristics of genomic regions where genes have been independently lost in multiple lineages. With a comprehensive scan of gene phylogenies of vertebrates with a careful inspection of evolutionary gene losses, we identified 813 human genes whose orthologs were lost in multiple mammalian lineages: designated 'elusive genes.' These elusive genes were located in genomic regions with rapid nucleotide substitution, high GC content, and high gene density. A comparison of the orthologous regions of such elusive genes across vertebrates revealed that these features had been established before the radiation of the extant vertebrates approximately 500 million years ago. The association of human elusive genes with transcriptomic and epigenomic characteristics illuminated that the genomic regions containing such genes were subject to repressive transcriptional regulation. Thus, the heterogeneous genomic features driving gene fates toward loss have been in place and may sometimes have relaxed the functional indispensability of such genes. This study sheds light on the complex interplay between gene function and local genomic properties in shaping gene evolution that has persisted since the vertebrate ancestor. Editor's evaluation The study provides a fundamental understanding of the driving forces behind gene losses in genome evolution and connects the propensity for gene losses to local genomic features like mutation rate and expression pattern. The methodology is compelling, as it identifies "elusive human genes" through independent gene losses in at least two mammalian lineages. The comparative genomics and statistical analyses are thorough and rigorous, making this study appealing to readers interested in exploring the global patterns and underlying mechanisms of gene fate evolution across the phylogenetic tree. https://doi.org/10.7554/eLife.82290.sa0 Decision letter Reviews on Sciety eLife's review process Introduction In the course of evolution, genomes continue to retain most genes with occasional duplications, while losing some genes (Blomme et al., 2006; Fernández and Gabaldón, 2020; Shen et al., 2018). This retention and loss can be interpreted as gene fate; genes are stably retained in the genome, but some factors may cause them to transition to a state where deletion occurs. Accordingly, identification of the factors allowing gene loss may facilitate our understanding of gene fate. Gene retention or loss has generally been considered to depend largely on the functional importance of the particular gene from the perspective of molecular evolutionary biology (Albalat and Cañestro, 2016; Bartha et al., 2018; Blanc et al., 2012; Liu et al., 2015; Olson, 1999; Sharma et al., 2018; Shen et al., 2018). Genes with indispensable functions have usually been retained with highly conserved sequences in genomes through rapid elimination of alleles that impair gene functions (Hirsh and Fraser, 2001; Krylov et al., 2003; Miyata et al., 1980; Pál et al., 2006). On the contrary, genes with less important functions are likely to accept more mutations and structural variations, which can degrade the original functions, leading to gene loss through pseudogenization or genomic deletion (Jordan et al., 2002; Yang et al., 2003). To date, gene loss has been imputed to the relaxation of functional constraints of individual genes. Gene loss has further been revealed to drive phenotypic adaptation in various organisms (Albalat and Cañestro, 2016; Olson, 1999), as well as in a gene knockout collection of yeasts in culture (Giaever and Nislow, 2014; Maclean et al., 2017). To uncover the association between fates and functional importance of the genes, molecular evolutionary analyses have been conducted at various scales, from gene-by-gene to genome-wide. A number of studies have revealed that the genes with reduced non-synonymous substitution rates (or KA values) and ratios of non-synonymous to synonymous substitution rates (KA/KS ratios) are less likely to be lost (Jordan et al., 2002; Yang et al., 2003). A genome-wide comparison of duplicated genes in yeast revealed larger KA values for those lost in multiple lineages than those retained by all the species investigated (Byrne and Wolfe, 2007). Other comprehensive studies of gene loss across metazoans and teleosts revealed that the genes expressed in the central nervous system are less prone to loss (Fernández and Gabaldón, 2020; Roux et al., 2017). These observations again suggest that gene fate depends on the functional constraints of a particular gene. Besides functional constraints, several studies have identified the genes lost independently in multiple lineages, revealing that the genomic regions containing these genes 'prefer' particular characteristics associated with structural instability (Cortez et al., 2014; Hughes et al., 2012; Lewin et al., 2021; Maeso et al., 2016). In mammals, tandemly arrayed homeobox genes derived from the Crx gene family were lost in multiple species (Lewin et al., 2021; Maeso et al., 2016). The findings suggest that genomic features containing tandem duplications facilitate unequal crossing over, leading to frequent gene loss. Mammalian chromosome Y, which contains abundant repetitive elements and continues to reduce in size, has lost a considerable number of genes (Cortez et al., 2014; Hughes et al., 2012). In the stickleback genome, a Pitx1 enhancer was independently lost in multiple lineages inhabiting freshwater due to its genomic location in a structurally fragile site, leading to recurrent loss of pelvic fins (Xie et al., 2019). Genes and genomic elements in such particular regions may be prone to loss in a more neutral manner than the relaxation of functional importance or via functional adaptations. Accordingly, these studies focusing on the particular genomic regions led us to search for the common features in genomes that potentially facilitate gene loss. Genome-wide scans have revealed heterogeneous distributions of a variety of sequence and structural features so far, for example, base composition (Bernardi and Bernardi, 1986; Cohen et al., 2005; Katzman et al., 2011), the frequency of repetitive elements (Korenberg and Rykowski, 1988; Medstrand et al., 2002), and DNA-damage sensitivity induced by replication inhibitors (Debatisse et al., 2012; Helmrich et al., 2006). However, the extent to which these characteristics are associated with gene fates has not been understood well at a genome-wide level. The accumulation of near-complete genome assemblies for various organisms facilitates comprehensive taxon-wide analysis of gene loss (Fernández and Gabaldón, 2020; Guijarro-Clarke et al., 2020; Rice and McLysaght, 2017). Along with this motivation, we recently performed a comprehensive analysis on the fate of paralogs generated via the two-round whole-genome duplications in early vertebrates (Hara et al., 2018a). The results revealed that the genes retained by reptiles but lost in mammals and Aves rapidly accumulated not only non-synonymous but also synonymous substitutions in comparison with the counterparts retained by almost all the vertebrates examined, indicating that those genes prone to loss show increasing mutation rates. Furthermore, these loss-prone genes were located in genomic regions with high GC contents, high gene densities, and high repetitive element frequencies. These findings suggest that the fates of those genes are influenced not only by functional constraints but also by intrinsic genomic characteristics. Because the findings were restricted to a set of particular genes, they prompted us to examine whether this trend is associated with gene fates on a genome-wide scale. In this study, we inferred molecular phylogenies of vertebrate orthologs to systematically search for the genes harboring different fates in the human genome. We previously referred to the nature of genes prone to loss as 'elusive' (Hara et al., 2018a; Hara et al., 2018b). In this study, we define the elusive genes as those that are retained by modern humans but have been lost independently in multiple mammalian lineages. As a comparison of the elusive genes, we retrieved the genes that were retained by almost all of the mammalian species examined and defined them as 'non-elusive,' representing those persistent in the genomes. We conducted a careful search for gene loss to reduce the false discovery rate (FDR), which is usually caused by incomplete sequence information (Botero-Castro et al., 2017; Deutekom et al., 2019). By comparing the genomic regions containing these genes, we uncovered genomic characteristics relevant to gene loss. We associated the elusive genes with a variety of findings from deep sequencing analyses of the human genome, including transcriptomics, epigenomics, and genetic variations. These data assisted us to understand how intrinsic genomic features may affect gene fate, leading to gene loss by decreasing the expression level and eventually relaxing the functional importance of 'elusive' genes. Results Identification of human 'elusive' genes We defined an 'elusive' gene as a human protein-coding gene that existed in the common mammalian ancestors but was lost independently in multiple mammalian lineages (Figure 1; see 'Materials and methods' for details). We searched for such genes by reconstructing phylogenetic trees of vertebrate orthologs and detecting gene loss events within the individual trees. To search for elusive genes, we paid close attention to distinguishing true evolutionary gene loss from falsely inferred gene loss caused by insufficient genome assembly, gene prediction, and orthologous clustering (Botero-Castro et al., 2017; Deutekom et al., 2019), as described below. Figure 1 Download asset Open asset Detection of 'elusive' genes. (a) Pipeline of ortholog group clustering and gene loss detection. (b) Definition of an elusive gene schematized with ortholog presence/absence pattern referring to a taxonomic hierarchy. Red and orange crosses denote the gene loss in the common ancestor of a taxon and the loss specific to a single species, respectively. (c) A representative phylogeny of the elusive gene encoding Chitinase 3-like 2 (CHI3L2). Taxa shown in the tree were used to investigate the presence or absence of orthologs. The Sciuromorpha, Hystricognathi, Eulipotyphla, Carnivora, and Chiroptera are absent from the tree, indicating that the CHI3L2 orthologs were lost somewhere along the branches framed in gray in the tree. In addition, the orthologs of many members of the Myomorpha were not found, suggesting that gene loss occurred in this lineage. We first produced highly complete orthologous groups comprised of nearly complete gene sets. We merged multiple gene annotations of a single species followed by assessments of the completeness of the gene sets (Figure 1a). Using these gene sets, we then created two sets of ortholog groups with different methods and merged them into a single set (Figure 1a). In searching for gene loss events, we restricted our study to those that occurred in the common ancestors of particular taxonomic groups. This procedure relieved false identifications of gene loss in a species or an ancestor of a lower taxonomic hierarchy caused by incomplete genomic information (Figure 1b). We integrated gene annotations from Ensembl, RefSeq, and the sequence repositories of individual genome sequencing projects to produce gene annotations for 114 mammalian and 132 non-mammalian vertebrates. From these, we selected the annotations of 101 and 90 species, respectively, that exhibited high completeness in the BUSCO assessment (Simão et al., 2015; Supplementary Table S1 in Supplementary file 1a). Using these gene sets, clustering of ortholog groups was conducted by OrthoFinder, and these groups were integrated into the ortholog groups provided by the Ensembl Gene Tree. This integration resulted in 50,768 vertebrate ortholog groups. Phylogenetic tree inference of the integrated ortholog groups and pruning of the individual trees based on gene duplications resulted in 17,495 mammalian ortholog groups that contained human genes. We classified the mammalian species into 15 taxonomic groups ranging from order to family (listed in Table S1; Supplementary file 1a). For the individual mammalian orthologs, we searched for the taxa in which the gene was absent in all the species examined (Figure 1b). We interpreted this gene absence as an evolutionary loss that occurred in the common ancestor of the taxon. Validating the gene loss through an ortholog search in genome assemblies and synteny-based ortholog annotations, we extracted the ortholog groups that were retained by humans but were lost independently in the common ancestors of at least two taxa (Figure 1c). Hereafter we call the human genes belonging to these ortholog groups 'elusive genes.' To compare these, we also selected the ortholog groups that contained all of the mammals examined including single-copy human genes. We called these 'non-elusive genes.' This comprehensive scan of gene phylogenies resulted in 813 elusive and 8050 non-elusive genes (Supplementary Table S2; Supplementary file 2). Genomic signatures of the human elusive genes The loss-prone nature of the elusive genes suggests a relaxation of their functional constraints. To uncover the molecular evolutionary characteristics associated with each elusive gene, we computed synonymous and non-synonymous substitution rates in coding regions, namely KS and KA, respectively, between human and chimpanzee and mouse orthologs for the elusive and non-elusive genes. In addition, we computed nucleotide substitution rates for introns (KI) between human and chimpanzee (Pan troglodytes) orthologs and compared them between the elusive and non-elusive genes. The results showed larger KA values in the ortholog pairs of the elusive genes than in those of the non-elusive genes (Figure 2a, Figure 2—figure supplement 1). This indicates a rapid accumulation of amino acid substitutions in the elusive genes, potentially accompanied by the relaxation of functional constraints. Our analysis further illuminated larger KS and KI values for the elusive genes than in the non-elusive genes (Figure 2b and c, Figure 2—figure supplement 1). Importantly, the higher rate of synonymous and intronic nucleotide substitutions, which may not affect changes in amino acid residues, indicates that the elusive genes are also susceptible to genomic characteristics independent of selective constraints on gene functions. Figure 2 with 1 supplement see all Download asset Open asset Genomic and evolutionary characteristics of elusive genes. Distributions of non-synonymous, synonymous, and intronic nucleotide substitution rates, namely KA (a), KS (b), and KI (c) values, respectively, between the human–chimpanzee orthologs of the elusive and non-elusive genes. Distribution of gene length (d) and GC content (e) of the human elusive and non-elusive genes. (f) Distribution of gene density in the genomic regions where the human elusive and non-elusive genes are located. The plots consist of 249 elusive and 5145 non-elusive genes that retained chimpanzee orthologs (a, b), 473 and 4626 of those which harbored introns aligned with the chimpanzee genome (c; see 'Materials and methods'), and all of the 813 elusive and 8050 non-elusive genes (d–f). Diamonds and bars within violin plots indicate the median and range from the 25th to 75th percentile, respectively. To further scrutinize the characteristics reflecting the genomic environment rather than gene function, we analyzed genomic characteristics that may distinguish the elusive from non-elusive genes. A comparison between these two categories revealed shorter gene-body lengths and higher GC contents of elusive rather than non-elusive genes (Figure 2d and e). Furthermore, a scan of intragenomic gene distribution revealed that the elusive genes were located in the genomic regions with high gene density compared with the non-elusive genes (Figure 2f). Our findings indicate that such elusive genes have distinct characteristics in the human genome. These genomic characteristics, as well as high nucleotide substitution rates, were consistent with the findings in our genome analyses using the amniote and elasmobranch genomes (Hara et al., 2018a; Hara et al., 2018b). Tracing elusiveness back along the vertebrate evolutionary tree The origins of the human elusive genes can be traced back along the evolutionary tree, at least to the mammalian common ancestor. To investigate possible antiquities of the genomic properties associated with elusive genes, we investigated their orthologs in non-mammalian vertebrates by scrutinizing the ortholog groups used for elusive gene identification. We found that 152 out of 813 elusive genes originated in mammalian lineages, and this proportion was larger than those of the elusive genes (65 out of 8050, p=2.50 × 10-110), indicating that the elusive genes are more abundant in recently born genes than non-elusive genes. We then selected 517 elusive and 7900 non-elusive genes that originated in the common ancestors of jawed vertebrates or earlier. These subsets allowed us to examine the degree of retention of non-mammalian vertebrate orthologs in the elusive and non-elusive genes. On average, approximately 40% of these elusive genes were found to be retained by non-mammalian vertebrates, while this proportion increased up to 90% for the non-elusive genes. (Figure 3—figure supplement 1a). In the coelacanth, gar, and shark, the orthologs of the elusive genes were less frequently retained by all the species than those of the non-elusive ones (Figure 3—figure supplement 1b). The results suggest that the origins of the loss-prone propensity of the elusive genes potentially date back to the period long before the emergence of the Mammalia. We further examined the genomic characteristics associated with the human elusive genes in the vertebrate orthologs. In all the species examined, orthologs of the elusive genes exhibited high GC content and compact gene bodies. Additionally, in most of these species, the orthologs of elusive genes were located in genomic regions with high gene density compared with orthologs of the non-elusive genes (Figure 3, Figure 3—figure supplement 2). In addition, we computed KS and KA values between the orthologs of the vertebrate species and their close relatives for elusive and non-elusive genes. In any of the species pairs except for avians, the orthologs of the elusive genes were found to harbor higher KA and KS values than those of the non-elusive gene orthologs (Figure 3, Figure 2—figure supplement 1). These observations indicate that these genomic characteristics probably originated before the emergence of gnathostomes, a monophyletic group of chondrichthyan and bony vertebrates, and have been retained for approximately 500 million years. Figure 3 with 2 supplements see all Download asset Open asset Long-standing characteristics of elusive genes. Retention of the genomic and evolutionary characteristics of the human elusive genes across vertebrates. The individual round squares with arrows indicate significant increases or decreases of the distribution of particular characteristics in the orthologs of the human elusive genes and their flanking regions compared with those of the non-elusive genes in these selected vertebrate genomes. For the chimpanzee and mouse genomes, KA and KS values were computed between the human elusive genes and the orthologs of these mammals. For non-mammalian species, these values were computed with ortholog pairs for the elusive/non-elusive genes between the corresponding species and their closely related species: turkey for chicken, green anole for central bearded dragon, and whale shark for bamboo shark. Distributions of these metrics for non-human species are shown in Figure 2—figure supplement 1 and Figure 3—figure supplement 2. Species name: mouse, Mus musculus; chicken, Gallus gallus; central bearded dragon, Pogona vitticeps; Western clawed frog, Xenopus tropicalis; coelacanth, Latimeria chalumnae; spotted gar, Lepisosteus oculatus; bamboo shark, Chiloscyllium plagiosum. Abundant polymorphism in elusive genes The observation of large KS and KA values in the elusive genes prompted us to examine the extent to which these genes have accommodated genetic variations in modern humans. Large-scale human genome resequencing projects have identified a huge number of genetic variations, from rare to common, and from single-nucleotide variants (SNVs) to chromosome-scale structural variants, facilitating tackling this issue. We retrieved copy number variants (CNVs) and rare SNVs in the human genome from the Database of Genomic Variants, release 2016-08-31 (MacDonald et al., 2014) and dbSNP release 147 (Sherry et al., 2001), respectively, and computed their densities in the individual genic regions. We found that the genic regions of the human elusive genes contained abundant rare SNVs, as well as deletion and duplication CNVs, compared with those of the non-elusive genes (Figure 4a–c). This result suggests that genomic regions containing the elusive genes are not only prone to loss but also to duplication. Figure 4 Download asset Open asset Genetic variations of the elusive and non-elusive genes within human populations. Comparison of the density of rare single-nucleotide variants (SNVs) (a), deletion copy number variants (CNVs) (b), duplication CNVs (c), and Z-scores of synonymous (d), missense (e), and loss-of-function variants (f). We used opposite numbers of the Z-scores in d–f so that the elusive genes have higher values than non-elusive genes as in Figure 2a, b, c, e, f and Figure 3a–c. (a–c) 813 elusive genes and 8050 non-elusive genes were used. (d–f) 544 elusive genes and 7303 non-elusive genes for which genetic variants were available in GnomAD were used. Diamonds and bars within violin plots indicate the median and range from 25th to 75th percentile, respectively. To evaluate the functional consequences of abundant genetic variants in the elusive genes, we investigated genetic variations stored in the gnomAD v. 2.1 database, a repository containing >120,000 exome and >15,000 whole-genome sequences of human individuals (Karczewski et al., 2021). This database classifies SNVs in coding regions into three and the loss-of-function contains and mutations in The gnomAD a an representing the of SNVs for individual and values denote or more mutations in a coding than (Figure Accordingly, the for mutations and loss-of-function mutations of the individual genes indicates the degree of larger values genes to while ones suggest functional We found lower Z-scores of missense and loss-of-function mutations opposite numbers of Z-scores in Figure and in the human elusive genes than in the non-elusive genes, suggesting that the elusive genes are more and potentially to Additionally, opposite numbers of Z-scores of synonymous mutations of the human elusive genes were higher than those of the non-elusive genes (Figure This the high mutability of genomic regions containing elusive genes, as in the KS of elusive genes To further investigate how the human elusive genes have functional we examined their expression For this we compared gene expression of the from the database v. et al., between the elusive and non-elusive genes. For individual genes, we computed the million values these as the expression level. For expression we which is as an of species in the based on the proportion of values across the As shown in the density plots of the individual genes these two in Figure most of the non-elusive genes large and Thus, most non-elusive genes are expressed at By the density of the elusive genes an with and values, indicating that the genes in this were not at least in The also showed of values, which contained the genes expressed in a single or a A analysis was performed with the single data et al., revealing that the expression of the elusive and non-elusive genes for the were with those of the (Figure Our findings that some elusive genes harbor and restricted expression that less which are in the non-elusive genes. Figure with 1 supplement see all Download asset Open asset of elusive and non-elusive genes. The density plots of the expression and of elusive and non-elusive genes. The numbers of the elusive/non-elusive genes and those for which the expression were available are in each were computed via 2 × 2 numbers of elusive and non-elusive genes with 1 and The median million of each of the across individuals was retrieved from the database et al., and values of the were retrieved from the database et al., For the individual genes, and values were computed using these nature of elusive genes Our of the and restricted expression patterns of elusive genes prompted us to properties in this transcriptional regulation. we retrieved data on a variety of human from a genome including a repository that the comprehensive annotations of functional elements in the human genome 2012). Using this we the features of the genomic regions containing elusive genes (Figure Figure with supplements see all Download asset Open asset features of the elusive genes. Comparison of the distribution of density (a), length of the including the elusive or non-elusive genes (b), the replication based on (c), and with the computed from of the analyses were performed by using the sequencing data available Supplementary file 1b). (d) and were performed with was performed with and was performed with In the elusive gene indicates the elusive genes with restricted 1; Figure for individual indicate the comparison between the elusive and non-elusive genes and the between the elusive genes with 1 and those with 1 The results for are shown in Figure supplements For the individual characteristics, for multiple was performed for comparison in each We compared densities based on the for using sequencing an of regions in the genome, in gene and flanking regions between the elusive and non-elusive genes. In all of the examined in the results showed in the genomic regions including the elusive genes than in those including non-elusive genes, indicating that the elusive genes are likely to in genomic regions (Figure Figure supplement 1). We also searched for genomic elements with frequent potentially as et al., 2014) that the elusive or non-elusive genes. The result showed that a higher of the elusive genes of the than the non-elusive genes for all the investigated (Figure Figure supplement

The choice of arboreal escape paths and its consequences for the locomotor behaviour of four species of Anolis lizards

Thermal comfort and adaptation of the elderly in free-running environments in Shanghai, China

Circadian rhythms are regulated by an internal clock, which is itself synchronized to environmental cues such as light and temperature. It is widely assumed that the circadian system is adapted to local cues, which vary enormously across habitats, yet the comparative data necessary for testing this idea are lacking. We examined photic and thermal resetting of the circadian clock in five species of Anolis lizards whose microhabitats differ in the amounts of sun and shade. The primary circadian oscillator in Anolis is the pineal gland, which produces the hormone melatonin. A flow-through culture system was employed to measure rhythmic melatonin output from individually cultured pineal glands. All species showed temperature-compensated circadian rhythms of pineal melatonin. Light caused significant phase delays of the melatonin rhythm, and this effect varied among species. Controlling for phylogenetic differences, the results indicate that the pineal glands of shade-dwelling species are more sensitive to photic resetting than species living in more brightly illuminated habitats. The differences were not due to variation in free-running period, but may be due to variation in oscillator phase and/or robustness. Surprisingly, thermal resetting was not statistically significant. Overall, the results suggest that the Anolis circadian system is adapted to photic habitat.

In order to analyze the thermal environment and its influence on workers’ thermal adaptation, a field study was conducted in a rubber factory during winter. Indoor and outdoor environmental parameters were measured and subjective questionnaire surveys were collected. The study was conducted from November to January the next year. During the survey, indoor temperature was in the range of 12.6 to 21.7°C and indoor air velocity ranged from 0.15 to 0.3 m/s. The clothing insulation during heating period was between 0.85-0.9 clo, while it was between 1.21-1.33 clo during pre-heating period. The estimated metabolic rate was around 2-2.2 met. Analysis showed that the thermal sensation vote (TSV) was higher than that predicted by PMV. The neutral temperature difference between TSV and PMV was 4.8°C. The thermal comfort and thermal adaptation of workers in winter were systematically analyzed and a thermal adaptive model was proposed. Basis on the adaptive model, the comfort temperature range of workers was suggested.

Thermal perception, adaptation and attendance in a public square in hot and humid regions

Schoener, Thomas W. (Biological Laboratories, Harvard Univ., Cambridge, Mass. 02138) 1969. Size pattern in West Indian Anolis lizards: I. Size and species diversity. Syst. Zool., 18:386-401.-Anolis lizard species have solitary populations on certain West Indian islands. These populations have a narrow range in mean body size, very different for the two sexes, though they inhabit islands varying greatly in area and environmental diversity. Smallsized exceptions to this uniformity are northerly. Sizes of males for solitary forms are collectively significantly larger than sizes of males on the richest islands. With increasing species diversity from island to island, species size distributions for males irregularly decrease in median but increase in range and skewness. On the three richest islands, smaller species are significantly more often restricted in geographic range. From simple assumptions about competition for resources, a relation is derived which holds that snout-vent length or some power thereof for a given species is equal to some multiple of the reciprocal of the number of closely related species on its island plus some constant. This relation is shown to better describe data than two alternatives. The ratio of the length of the principal trophic structure (the head) to the entire body length of a given species is sometimes but not always predictable from the number of congeneric species on its island. [Anolis; West Indies; size; diversity; convergence; evolution]. Among terrestrial vertebrates, West Indian lizards of the genus Anolis are notable in numerical abundance, species diversity, and observability. These features have stimulated abundant research on the ecology and evolution of this genus, mostly yet unpublished (see Williams, in press, for a review). Recently, E. E. Williams and I were struck by the opportunity which Anolis offered for making the sort of inductive generalizations about interspecific size differences in trophic structures and total bulk that have been made for birds (Lack, 1947; Hutchinson, 1959; Klopfer and MacArthur, 1961; Schoener, 1965; Grant, 1968 and included references). Our aims were twopronged. First, the resulting set of patterns describing size differences should extend or delimit the domain of tendencies noted for birds. But more importantly, the extensive lode of habitat and distributional information for this more narrowly defined group should permit a more exact statement of t-he relation of spatial overlap to size differences. This paper considers the possible effects of three major environmental factors-number of sympatric congeners, latitude, and island size-and several minor ones on the absolute and relative body sizes of males and females. Other results are presented elsewhere (Schoener,

Thermal history and adaptation: Does a long-term indoor thermal exposure impact human thermal adaptability?

Although the maximal speeds of straight-ahead running are well-documented for many species of Anolis and other lizards, no previous study has experimentally determined the effects of turning on the locomotor performance of a lizard. Anolis lizards are a diverse group of arboreal species, and the discrete paths created by networks of perches in arboreal environments often force animals to turn in their natural habitats. For three species of Anolis with similar overall body size but different shape, we quantified the escape locomotor performance for arboreal locomotion on 4.8 cm diameter perches that were straight (0 degrees ) or had turning angles of 30 degrees and 90 degrees. The turning angle had widespread significant effects that were often species-dependent. This was shown by measuring the average gross velocity (including the times while the lizards paused) of the three species covering the middle 30 cm of a racetrack with either 30 degrees or 90 degrees turns. The results were expressed as a percentage of the gross velocity over the same distance on a straight racetrack. The values obtained for A. grahami (99 % for 30 degrees turns and 79 % for 90 degrees turns) showed a smaller effect of turning angle than for A. lineatopus (79 % for 30 degrees turns and 50 % for 90 degrees turns) and A. valencienni (74 % for 30 degrees turns and 48 % for 90 degrees turns). Consequently, the rank order of species based on speed depended on the angle of the turn. Some of the magnitudes of decreased locomotor speed associated with turning exceeded those reported previously for the effects of decreasing perch diameter for these species. For all species, more pausing occurred with increased turning angle, with the twig ecomorph (A. valencienni) pausing the most. Approximately half the individuals of each species jumped to traverse the 90 degrees turn, but some of the potential benefits of jumping for increasing speed were offset by pauses associated with preparing to jump or recovering balance immediately after a jump. The tail of Anolis lizards may facilitate the substantial rotation (>60 degrees ) of the body that often occurred in the airborne phase of the jumps.

The 3′-nucleotides of flavivirus genomic RNA form a conserved secondary structure

Epigenetic mechanisms play a major role in heterosis, partly as a result of the remodeling of epigenetic modifications in F1 hybrids. Based on chromatin immunoprecipitation-sequencing (ChIP-Seq) analyses, we show that at the allele level extensive histone methylation remodeling occurred for a subset of genomic loci in reciprocal F1 hybrids of Oryza sativa (rice) cultivars Nipponbare and 93-11, representing the two subspecies japonica and indica. Globally, the allele modification-altered loci in leaf or root of the reciprocal F1 hybrids involved ˜12-43% or more of the genomic regions carrying either of two typical histone methylation markers, H3K4me3 (>21000 genomic regions) and H3K27me3 (>11000 genomic regions). Nevertheless, at the total modification level, the majority (from ˜43 to >90%) of the modification-altered alleles lay within the range of parental additivity in the hybrids because of concerted alteration in opposite directions, consistent with an overall attenuation of allelic differences in the modifications. Importantly, of the genomic regions that did show non-additivity in total modification level by either marker in the two tissues of hybrids, >80% manifested transgressivity, which involved genes enriched in specific functional categories. Extensive allele-level alteration of H3K4me3 alone was positively correlated with genome-wide changes in allele-level gene expression, whereas at the total level, both H3K4me3 and H3K27me3 remodeling, although affecting just a small number of genes, contributes to the overall non-additive gene expression to variable extents, depending on tissue/marker combinations. Our results emphasize the importance of allele-level analysis in hybrids to assess the remodeling of epigenetic modifications and their relation to changes in gene expression.

Ectotherms are thought to be particularly vulnerable to climate change as they rely directly on environmental temperatures to regulate their physiology. One of the pathways by which ectotherms can alter their physiology in a warming environment is through phenotypic plasticity, which is usually treated as resulting from interactions between the organism's genetics and the environment. However, ectotherms also host communities of microbes which can change quickly within the host and affect host physiology. To date, little is known about the extent to which gut microbes affect thermal plasticity in the non-model host organisms that will be the most affected by climate change. We investigated relationships between gut microbiome composition and host heat tolerance plasticity in three species of Anolis lizards: Anolis cristatellus, Anolis sagrei and Anolis carolinensis. We brought wild-caught lizards into the lab and tested for (1) effects of experimental warming on the gut microbiomes and (2) associations between microbiome composition and compositional dynamics with heat tolerance and its plasticity across host individuals and species. We found that each anole species hosted a distinct gut microbial community, but that all host species had microbiomes that were largely resilient to temperature increases. However, several key aspects of microbiome composition were correlated with baseline host heat tolerance. Finally, microbiome composition and its stability were associated with the magnitude of plasticity in host heat tolerance. Our results indicate that gut microbes may play a role in the ability of ectotherms to mount plastic responses to rapidly changing thermal environments.

The urban heat island effect, where urban areas exhibit higher temperatures than less-developed suburban and natural habitats, occurs in cities across the globe and is well understood from a physical perspective and at broad spatial scales. However, very little is known about how thermal variation caused by urbanization influences the ability of organisms to live in cities. Ectotherms are sensitive to environmental changes that affect thermal conditions, and therefore, increased urban temperatures may pose significant challenges to thermoregulation and alter temperature-dependent activity. To evaluate whether these changes to the thermal environment affect the persistence and dispersal of ectothermic species in urban areas, we studied two species of Anolis lizards (Anolis cristatellus and Anolis sagrei) introduced to Miami-Dade County, FL, USA, where they occur in both urban and natural habitats. We calculated canopy openness and measured operative temperature (Te ), which estimates the distribution of body temperatures in a non-thermoregulating population, in four urban and four natural sites. We also captured lizards throughout the day and recorded their internal body temperature (Tb ). We found that urban areas had more open canopies and higher Te compared to natural habitats. Laboratory trials showed that A.cristatellus preferred lower temperatures than A.sagrei. Urban sites currently occupied by each species appear to lower thermoregulatory costs for both species, but only A.sagreihad field Tb that were more often within their preferred temperature range in urban habitats compared to natural areas. Furthermore, based on available Te within each species' preferred temperature range, urban sites with only A.sagrei appear less suitable for A.cristatellus, whereas natural sites with only A.cristatellus are less suitable for A.sagrei. These results highlight how the thermal properties of urban areas contribute to patterns of persistence and dispersal, particularly relevant for studying species invasions worldwide.

S-adenosylmethionine Levels Regulate the Schwann Cell DNA Methylome

Thermal adaptation and thermal environment in university classrooms and offices in Harbin